De novo genome assembly and annotation of Australia's largest freshwater fish, the Murray cod (Maccullochella peelii) from Illumina and Nanopore sequencing reads

Background: One of the most iconic Australian fish is the Murray cod, Maccullochella peelii (Mitchell, 1838), a freshwater species that can grow to (similar to)1.8 metres in length and live >= 48 years of age. The Murray cod is of conservation concern as a result of strong population contractions, but is also popular for recreational fishing and is of growing aquaculture interest. In this study, we report the whole genome sequence of the Murray cod to support ongoing population genetics, conservation and management-related research, as well as to understand better the evolutionary ecology and history of the species. Findings: A draft Murray cod genome of 633 Mbp (N-50=109,974bp; BUSCO and CEGMA completeness of 94.2% and 91.9%, respectively) with an estimated 148 Mbp of putative repetitive sequences was assembled from the combined sequencing data of two fish individuals with an identical maternal lineage. 47.2 Gb of Illumina HiSeq data and 804 Mb of Nanopore data were generated from the first individual while 23.2 Gb of Illumina MiSeq data were from the second individual. The inclusion of Nanopore reads for scaffolding followed by subsequent gap-closing using Illumina data led to a 29% reduction in the number of scaffolds and a 55% and 54% increase in the scaffold and contig N50, respectively. We also report the first transcriptome of Murray cod that was subsequently used to annotate the Murray cod genome leading to the identification of 26,539 protein-coding genes. Conclusions: We present the whole genome of the Murray cod and anticipate this will be a catalyst for a range of genetic, genomic and phylogenetic studies of the Murray cod and more generally other fish species of Percichthydae family.